I've been using gnuplot since 1995 and it is still my #1 choice for data plotting. I have used it for quite a few scientific papers (physics/chemical physics) and I'm happy to see that gnuplot has grown with me over the years. There is some learning curve to overcome if you want to make really nice graphs, which often require manual tweaks, but I've found that the learning curve is by no means easier for alternatives such as Python+mathplotlib, Excel (horrible defaults out of the box), or Matlab.